1MO5

RECA-ATP-GAMMA-S-MG COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural studies on MtRecA-nucleotide complexes: Insights into DNA and nucleotide binding and the structural signature of NTP recognition

Datta, S.Ganesh, N.Chandra, N.R.Muniyappa, K.Vijayan, M.

(2003) Proteins 50: 474-485

  • DOI: 10.1002/prot.10315
  • Primary Citation of Related Structures:  1MO3, 1MO4, 1MO6
  • Also Cited By: 1UBF, 2G88, 2ODN, 2ODW, 2OE2, 2OEP, 2OES, 2OFO, 4OQF, 4PO1, 4PO8, 4PO9, 4POA, 4PPF, 4PPG, 4PPN, 4PPQ, 4PQF, 4PQR, 4PQY, 4PR0, 4PSA, 4PSK, 4PSV, 4PTL

  • PubMed Abstract: 
  • RecA protein plays a crucial role in homologous recombination and repair of DNA. Central to all activities of RecA is its binding to Mg(+2)-ATP. The active form of the protein is a helical nucleoprotein filament containing the nucleotide cofactor and ...

    RecA protein plays a crucial role in homologous recombination and repair of DNA. Central to all activities of RecA is its binding to Mg(+2)-ATP. The active form of the protein is a helical nucleoprotein filament containing the nucleotide cofactor and single-stranded DNA. The stability and structure of the helical nucleoprotein filament formed by RecA are modulated by nucleotide cofactors. Here we report crystal structures of a MtRecA-ADP complex, complexes with ATPgammaS in the presence and absence of magnesium as well as a complex with dATP and Mg+2. Comparison with the recently solved crystal structures of the apo form as well as a complex with ADP-AlF4 confirms an expansion of the P-loop region in MtRecA, compared to its homologue in Escherichia coli, correlating with the reduced affinity of MtRecA for ATP. The ligand bound structures reveal subtle variations in nucleotide conformations among different nucleotides that serve in maintaining the network of interactions crucial for nucleotide binding. The nucleotide binding site itself, however, remains relatively unchanged. The analysis also reveals that ATPgammaS rather than ADP-AlF4 is structurally a better mimic of ATP. From among the complexed structures, a definition for the two DNA-binding loops L1 and L2 has clearly emerged for the first time and provides a basis to understand DNA binding by RecA. The structural information obtained from these complexes correlates well with the extensive biochemical data on mutants available in the literature, contributing to an understanding of the role of individual residues in the nucleotide binding pocket, at the molecular level. Modeling studies on the mutants again point to the relative rigidity of the nucleotide binding site. Comparison with other NTP binding proteins reveals many commonalties in modes of binding by diverse members in the structural family, contributing to our understanding of the structural signature of NTP recognition.


    Related Citations: 
    • Crystal Structures of Mycobacterium Tuberculosis Reca and its Complex with Adp-Alf4: Implications For Decreased ATPase Activity and Molecular Aggregation
      Datta, S.,Prabu, M.,Vaze, M.B.,Ganesh, N.,Chandra, N.R.,Muniyappa, K.,Vijayan, M.
      (2000) Nucleic Acids Res. 28: 4964
    • Functional Characterization of the Precursor and Spliced Forms of Reca Protein of Mycobacterium Tuberculosis.
      Ajay Kumar, R.,Vaze, M.,Chandra, N.R.,Vijayan, M.,Muniyappa, K.
      (1996) Biochemistry 35: 1793


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RecA
A
350Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: recA
EC: 3.1.-.-
Find proteins for P9WHJ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHJ3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download SDF File 
Download CCD File 
A
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.188 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 108.032α = 90.00
b = 108.032β = 90.00
c = 72.475γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-02-15
    Type: Non-polymer description
  • Version 1.4: 2017-08-16
    Type: Refinement description, Source and taxonomy